The ability of oligonucleotides and their analogs to interact with complementary nucleic acid sequences has been used to design reagents which can bind to functional regions of mRNA or precursor mRNA and, as a consequence of this binding interaction, inhibit the expression or function of the mRNA both in vitro and in cells in culture. The goal of this project is to extend this concept to the design of oligonucleotide analogs which can be used to disrupt gene expression at the DNA level. We will synthesize oligo-2'-amino' and 2'-methylamino-2'-deoxyribonucleotides. These oligomers are designed to be electroneutral at or near physiological pH and to form duplexes specifically with single stranded DNA (ssDNA). We will study the conformation of these electroneutral nucleic acid analogs in solution by nuclear magnetic resonance spectroscopy; study their interactions with single stranded DNA and RNA targets; and study their stability and uptake in simple cell culture systems. We will also synthesize oligonucleotide analogs containing modified bases which will enable the oligomer to "read" both purine and pyrimidine nucleotides in double stranded DNA (dsDNA) via the formation of triple stranded complexes and study their interactions with model dsDNA in vitro. The ability of the oligonucleotide analogs to inhibit and/or serve as substrates (primers) for DNA polymerase, will be determined. In addition to furthering our knowledge about the structure and biochemistry or nucleic acid analogs, the oligomers proposed in this application could serve as important research tools for the study of gene expression in DNA viruses and retroviruses, such as the human immunodeficiency virus, and could eventually find therapeutic applications.